Carbon quantum dots(CQDs) are widely used in fluorescence imaging due to their negligible toxicity, low-cost and excellent fluorescence properties. The fluorescence properties of CQDs are greatly affected by the synthesis method, passivation agent and reaction media. In this study, the nitrogen-doped CQDs(N-CQDs) were synthesized by a facile microwave-assisted method with citric acid(CA) as a carbon source and deep eutectic solvents as a N-dopant as well as the reaction solvent. After detailed characterizations, the as-prepared N-CQDs exhibited near spherical morphology with an average size of (2.64±0.55) nm. Besides, the abundant hydrophilic functional groups including hydroxyl, carboxyl, amine and quaternary ammonium were present on the surface of the N-CQDs. The N-CQDs displayed the excitation-dependent fluorescence feature under the excitation wavelength of 350–480 nm. Moreover, the N-CQDs could be efficiently uptaken by RAW264.7 cells and emitted bright green light. Meanwhile, the resultant N-CQDs showed the low cytotoxicity in living cells, suggesting the great potential in bio-imaging applications.